Press paws for the African wild dog

Today we are releasing the chromosome-length genome assembly for the African wild dog Lycaon pictus. African wild dogs are considered one of Africa’s most effective predators, boasting an 80% success rate with hunts; far higher than the 30% rate of lions [1]. They are classified as endangered by IUCN due to loss of habitat and susceptibility to disease spread by domestic animals [2].

This assembly was done in collaboration with Ellie Armstrong, Dmitri Petrov, Ryan Taylor, John Stuelpnagel, Peter Blinston and others from the Lycaon pictus whole genome shotgun sequencing project [3]. The genomic material for DNA-Seq was provided by Painted Dog Conservation, and the sample for Hi-C library preparation was donated by the Houston Zoo.

It must be noted that there is some disagreement in the literature about the karyotype for this species [4, 5]. We are grateful to Marlys Houck and Ann Misuraca from the San Diego Zoo Institute for Conservation Research for confirming our prediction for the 39 haploid chromosome count.

We also share an earlier version of this genome assembly, based on the version of the draft from (Armstrong et al., Gigascience, 2019), here. Check out the whole-genome alignments of the two assemblies to the dog genome canFam3.1 (Lindblad-toh et al., Nature, 2005), below!

Whole genome alignment of the chromosome-length genome assembly for the Lycaon pictus to the chromosomes of domestic dog, from (Lindblad-toh et al., Nature, 2005).

Hare-raising adventure in genome assembly

The California sea hare, Aplysia californica, is a species of gastropod molluscs found along the coast of California, United States, and northwestern Mexico. These sea slugs possess the largest nerve cells in the entire animal kingdom, making them a valuable model organism to study the neurobiology of learning and memory [1].

In 2003 Leonid L. Moroz (University of Florida) and Eric R. Kandel (Columbia University) initiated the sequencing of the whole genome of A. californica, which was approved as a priority by National Human Genome Research Institute in March 2005. The Broad Institute, using inbred lines of Aplysia (F4) raised by Tom Capo (NIH Aplysia facility) in collaboration with the Moroz lab generated the first draft assembly for the species in 2006, revised in 2009 and 2013 [2, 3]. Together with Leonid Moroz and his team at the University of Florida we are today releasing a chromosome-length assembly for A. californica based on the 2013 draft from the Broad Institute.

Check out whole-genome alignment of the new assembly to the 14 linkage groups of the channeled applesnail Pomacea canaliculata from (Liu et al., GigaScience, 2018), illustrating, for the first time ever, the conservation of chromosome content across 400 million years of gastropod evolution.

Whole-genome alignment of the new Aplysia californica assembly to the 14 linkage groups of Pomacea canaliculata, from (Liu et al., 2018).

No drama piranha

The red-bellied piranha, also known as the red piranha (Pygocentrus nattereri), is a species of piranha native to South America and a popular aquarium fish. Through media influence, the red-bellied piranha has developed a reputation as a ferocious predator, but scientists believe that the animals’ fearsome reputation has been exaggerated [1].

This week we are releasing the chromosome-length assembly for the red-bellied piranha, based on the work by W.C. Warren and M. Schartl [2]. We are grateful to Moody Gardens for the sample used for Hi-C library preparation!

Check out the alignments of the new assembly to the two most closely related fish genome assemblies out there: the Mexican tetra Astyanax mexicanus, from (McGaugh et al. Nat Commun., 2014), and the channel catfish Ictalurus punctatus, from (Liu et al. Nat Commun., 2016). Looks like the content of the chromosomes is largely preserved.

Whole genome alignments of the red-bellied piranha genome assembly to the assemblies of the Mexican tetra (left) and channel catfish (right).